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<html><head><title>Python: module data_model.cog</title>
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<font color="#ffffff" face="helvetica, arial">&nbsp;<br><big><big><strong><a href="data_model.html"><font color="#ffffff">data_model</font></a>.cog</strong></big></big></font></td
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><font color="#ffffff" face="helvetica, arial"><a href=".">index</a><br><a href="file:/home/lc6/pygenome/src/data_model/cog.py">/home/lc6/pygenome/src/data_model/cog.py</a></font></td></tr></table>
    <p><tt>COG&nbsp;module</tt></p>
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<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#fffff" face="helvetica, arial"><big><strong>Modules</strong></big></font></td></tr>
    
<tr><td bgcolor="#aa55cc"><tt>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</tt></td><td>&nbsp;</td>
<td width="100%"><table width="100%" summary="list"><tr><td width="25%" valign=top><a href="logging.html">logging</a><br>
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<font color="#ffffff" face="helvetica, arial"><big><strong>Classes</strong></big></font></td></tr>
    
<tr><td bgcolor="#ee77aa"><tt>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</tt></td><td>&nbsp;</td>
<td width="100%"><dl>
<dt><font face="helvetica, arial"><a href="__builtin__.html#object">__builtin__.object</a>
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<dt><font face="helvetica, arial"><a href="data_model.cog.html#Cog">Cog</a>
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<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="Cog">class <strong>Cog</strong></a>(<a href="__builtin__.html#object">__builtin__.object</a>)</font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt>Represent&nbsp;a&nbsp;COG&nbsp;family<br>
The&nbsp;class&nbsp;stored&nbsp;the&nbsp;genome&nbsp;record&nbsp;that&nbsp;hits&nbsp;on&nbsp;this&nbsp;COG<br>&nbsp;</tt></td></tr>
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<td width="100%">Methods defined here:<br>
<dl><dt><a name="Cog-__init__"><strong>__init__</strong></a>(self, name, length, category, desc)</dt><dd><tt>Constructor</tt></dd></dl>

<dl><dt><a name="Cog-add_hits"><strong>add_hits</strong></a>(self, genome_record)</dt><dd><tt>Append&nbsp;genome_record&nbsp;to&nbsp;this&nbsp;cog&nbsp;family<br>
&nbsp;<br>
Arguments:<br>
-&nbsp;`genome_record`:&nbsp;the&nbsp;record&nbsp;to&nbsp;be&nbsp;appended</tt></dd></dl>

<dl><dt><a name="Cog-get_hits_frequency"><strong>get_hits_frequency</strong></a>(self)</dt><dd><tt>Return&nbsp;an&nbsp;array&nbsp;of&nbsp;int&nbsp;that&nbsp;represents&nbsp;the&nbsp;frequency&nbsp;of&nbsp;every<br>
data&nbsp;point.&nbsp;The&nbsp;size&nbsp;of&nbsp;array&nbsp;is&nbsp;equal&nbsp;to&nbsp;cog&nbsp;length.</tt></dd></dl>

<dl><dt><a name="Cog-get_hits_range"><strong>get_hits_range</strong></a>(self)</dt><dd><tt>Return&nbsp;a&nbsp;list&nbsp;of&nbsp;genome&nbsp;records'&nbsp;(read,&nbsp;start,&nbsp;end)&nbsp;positions.</tt></dd></dl>

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Properties defined here:<br>
<dl><dt><strong>category</strong></dt>
<dd><dl><dt><a name="-<em>get</em>"><strong><em>get</em></strong></a> = _get_category(self)</dt></dl>
</dd>
</dl>
<dl><dt><strong>desc</strong></dt>
<dd><dl><dt><a name="-<em>get</em>"><strong><em>get</em></strong></a> = _get_desc(self)</dt></dl>
</dd>
</dl>
<dl><dt><strong>file_name</strong></dt>
<dd><dl><dt><a name="-<em>get</em>"><strong><em>get</em></strong></a> = _get_file_name(self)</dt></dl>
</dd>
<dd><dl><dt><a name="-<em>set</em>"><strong><em>set</em></strong></a> = _set_file_name(self, value)</dt></dl>
</dd>
</dl>
<dl><dt><strong>hitp</strong></dt>
<dd><dl><dt><a name="-<em>get</em>"><strong><em>get</em></strong></a> = _get_hitp(self)</dt></dl>
</dd>
<dd><dl><dt><a name="-<em>set</em>"><strong><em>set</em></strong></a> = _set_hitp(self, value)</dt></dl>
</dd>
</dl>
<dl><dt><strong>hits</strong></dt>
<dd><dl><dt><a name="-<em>get</em>"><strong><em>get</em></strong></a> = _get_hits(self)</dt></dl>
</dd>
</dl>
<dl><dt><strong>length</strong></dt>
<dd><dl><dt><a name="-<em>get</em>"><strong><em>get</em></strong></a> = _get_length(self)</dt><dd><tt>The&nbsp;size&nbsp;of&nbsp;COG&nbsp;family</tt></dd></dl>
</dd>
</dl>
<dl><dt><strong>name</strong></dt>
<dd><dl><dt><a name="-<em>get</em>"><strong><em>get</em></strong></a> = _get_name(self)</dt></dl>
</dd>
</dl>
<dl><dt><strong>number_of_hits</strong></dt>
<dd><dl><dt><a name="-<em>get</em>"><strong><em>get</em></strong></a> = _get_number_of_hits(self)</dt></dl>
</dd>
</dl>
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Data and other attributes defined here:<br>
<dl><dt><strong>__dict__</strong> = &lt;dictproxy object&gt;<dd><tt>dictionary&nbsp;for&nbsp;instance&nbsp;variables&nbsp;(if&nbsp;defined)</tt></dl>

<dl><dt><strong>__slotnames__</strong> = []</dl>

<dl><dt><strong>__weakref__</strong> = &lt;attribute '__weakref__' of 'Cog' objects&gt;<dd><tt>list&nbsp;of&nbsp;weak&nbsp;references&nbsp;to&nbsp;the&nbsp;<a href="__builtin__.html#object">object</a>&nbsp;(if&nbsp;defined)</tt></dl>

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<font color="#ffffff" face="helvetica, arial"><big><strong>Data</strong></big></font></td></tr>
    
<tr><td bgcolor="#55aa55"><tt>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</tt></td><td>&nbsp;</td>
<td width="100%"><strong>__author__</strong> = 'Lei Chen &lt;hide1713@gmail.com&gt;'</td></tr></table><p>
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<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#ffffff" face="helvetica, arial"><big><strong>Author</strong></big></font></td></tr>
    
<tr><td bgcolor="#7799ee"><tt>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</tt></td><td>&nbsp;</td>
<td width="100%">Lei&nbsp;Chen&nbsp;&lt;hide1713@gmail.com&gt;</td></tr></table>
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